A 73-year-old woman was admitted to our hospital with anterior acute myocardial infarction due to subacute thrombosis after coronary stenting with a zotarolimus-eluting stent (ZES), which is a newly developed drug-eluting stent that has been widely used since May 2009 in Japan. Five days before, she underwent implantation with a ZES in the left anterior descending artery due to stable angina pectoris. After stenting, the intravascular ultrasonography showed no malapposition from the proximal to the distal edge of the stent. She received aspirin 100 mg/day and clopidogrel 75 mg/day from 2 weeks before the stent was implanted. When we investigated the single nucleotide polymorphisms of CYP2C19 in this patient, both CYP2C19*2 and CYP2C19*3 were detected, and she was classified as a poor metabolizer. This report is the first to describe subacute stent thrombosis following the implantation of a newly developed ZES in a Japanese patient, which may be related to clopidogrel resistance.